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README.Rmd
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---
output:
md_document:
variant: gfm
html_preview: false
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE, echo=FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
# fig.width = 7,
# fig.height = 5,
warning = FALSE,
message = TRUE,
fig.path = "man/figures/",
out.width = "100%"
)
```
```{r echo=FALSE, results="hide", message=FALSE}
library("badger")
```
# tidymass <img src="man/figures/logo.png" align="right" alt="" width="120" />
```{r, echo = FALSE, results='asis'}
cat(
badge_cran_release("tidymass", "green"),
badge_code_size(ref = "tidymass/tidymass"),
badge_dependencies(),
badge_lifecycle()
# badge_cran_download("badger", "grand-total", "green"),
# badge_cran_download("badger", "last-month", "green"),
# badge_cran_download("badger", "last-week", "green")
)
```
## About
`tidymass` is a collections of R packages for mass spectrometry data processing, analysis.
<img src="man/figures/workflow_tidymass.jpg" align="middle" alt="" width = "80%"/>
## Installation
You can install `tidymass` from [Github](https://github.com/tidymass/tidymass).
```{r, eval=FALSE}
if(!require(devtools)){
install.packages("devtools")
}
devtools::install_github("tidymass/tidymass")
```
Then you can use `install_tidymass()` to install all the packages in `tidymass`.
```{r, eval=FALSE}
library(tidymass)
```
```{r, eval=FALSE}
tidymass::install_tidymass(from = "github", force = FALSE)
```
## Usage
Now, `tidymass` contains several packages:
--------
### metflow2 <img src="man/figures/metflow2_logo.png" align="left" alt="" width="120" />
If you use lipidflow in you publication, please cite this publication:
X. Shen, R. Wang, X. Xiong, Y. Yin, Y. Cai, Z. Ma, N. Liu, and Z.-J. Zhu* (Corresponding Author), Metabolic Reaction Network-based Recursive Metabolite Annotation for Untargeted Metabolomics, Nature Communications, 2019, 10: 1516.
--------
### metNormalizer <img src="man/figures/metnormalizer_logo.png" align="left" alt="" width="120" />
If you use lipidflow in you publication, please cite this publication:
X. Shen, R. Wang, X. Xiong, Y. Yin, Y. Cai, Z. Ma, N. Liu, and Z.-J. Zhu* (Corresponding Author), Metabolic Reaction Network-based Recursive Metabolite Annotation for Untargeted Metabolomics, Nature Communications, 2019, 10: 1516.
--------
### metID <img src="man/figures/metID_logo.png" align="left" alt="" width="120" />
If you use lipidflow in you publication, please cite this publication:
X. Shen, R. Wang, X. Xiong, Y. Yin, Y. Cai, Z. Ma, N. Liu, and Z.-J. Zhu* (Corresponding Author), Metabolic Reaction Network-based Recursive Metabolite Annotation for Untargeted Metabolomics, Nature Communications, 2019, 10: 1516.
--------
### lipidflow <img src="man/figures/lipidflow_logo.png" align="left" alt="" width="120" />
If you use lipidflow in you publication, please cite this publication:
X. Shen, R. Wang, X. Xiong, Y. Yin, Y. Cai, Z. Ma, N. Liu, and Z.-J. Zhu* (Corresponding Author), Metabolic Reaction Network-based Recursive Metabolite Annotation for Untargeted Metabolomics, Nature Communications, 2019, 10: 1516.
--------
## Need help?
If you have any quesitions about `tidymass`, please don't hesitate to email me (shenxt@stanford.edu).
<i class="fa fa-weixin"></i> [shenxt1990](https://www.shenxt.info/files/wechat_QR.jpg)
<i class="fa fa-envelope"></i> shenxt@stanford.edu
<i class="fa fa-twitter"></i> [Twitter](https://twitter.com/JasperShen1990)
<i class="fa fa-map-marker-alt"></i> [M339, Alway Buidling, Cooper Lane, Palo Alto, CA 94304](https://www.google.com/maps/place/Alway+Building/@37.4322345,-122.1770883,17z/data=!3m1!4b1!4m5!3m4!1s0x808fa4d335c3be37:0x9057931f3b312c29!8m2!3d37.4322345!4d-122.1748996)
## Citation
If you use tidymass in you publication, please cite this publication:
X. Shen, R. Wang, X. Xiong, Y. Yin, Y. Cai, Z. Ma, N. Liu, and Z.-J. Zhu* (Corresponding Author), Metabolic Reaction Network-based Recursive Metabolite Annotation for Untargeted Metabolomics, Nature Communications, 2019, 10: 1516.
[Web Link](https://www.nature.com/articles/s41467-019-09550-x).
Thanks very much!